Protein diets are required for the normal development of the reproductive system and their inadequacy or deficiency might have hazardous functional complications during maturational and developmental stages. The study was carried out to evaluate the effect of selenium (Se) and zinc (Zn) supplementation on the male and female reproductive organs of rats with postnatal protein malnutrition. Male and female weanling rats were randomly assigned to six groups respectively. The adequate protein diet rats were fed with 16% casein diet while the protein malnourished diet (PMD) rats were fed with 5% casein diet. After the 8th week of feeding, Se (sodium selenite; NaSeO) and Zn (zinc sulfate; ZnSO·7HO) were supplemented for 3 weeks. The growth curve of body weights, lipid profile, testosterone and progesterone level, Na-K-ATPase activity, oxidative stress, and antioxidant status were evaluated. The results showed that PMD reduced the body weights of male and female rats. It also reduced the activities of catalase and glutathione peroxidase in the testes, but reductions in superoxide dismutase and glutathione-S-transferase activities, glutathione, vitamins C and E, testosterone, and progesterone levels were observed in both the testes and ovaries. Furthermore, PMD increased the nitric oxide level in both organs and altered the plasma lipid profiles in both sexes. Se and Zn supplementation, however, restored almost all the alterations observed in all the parameters analyzed. In conclusion, Se and Zn supplementation protects the male and female reproductive organs of rats against postnatal protein malnutrition.